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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGGGGCGTCCACTTCCGGTGCCGAGAGCAGCGCCGTGGAGATGGGCACCGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAGgtaaacagaatgtttgcttctgtcctgtgtgcgctgcttgtagtgttaggccttgttagacgctgactgtcttatcgcattctgggcaaattggttgctg...

Basic information

species Zea mays
transcript GRMZM2G052546_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052546_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g01750.2 (Oryza sativa), 5'ss of exon 4
CCTGGGGCGTCCACTTCCGGTGCCGAGAGCAGCGCCGTGGAGATGGGCACCGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAGgtaaa----cagaatgt-ttgcttctgtcctgtgtgcgctgcttgtagtgttaggccttgttagacgctgactgtcttatcgcattctgggcaaattggttgctg
 | |||||||| |||||  | ||||||||  |||| ||||||  |||||| ||||| |||||   ||||||||| ||||||||||| ||||||||||||||||||    ||  |||  || | |     |  |      || | |  ||   | | |||||  ||   |    | | |   ||   |||     | ||||     
TCCGGGGCGTCTACTTCTAGCGCCGAGAGTGGCGCAGTGGAGGCGGGCACGGAGAAATCCGATACGTACAGCACCAACATGACGCAAGCTATGGGAGCAGgtaaagacccattatgccttacctgcaatcaatactacatgttagctgtaccacgacttgtcggattgtactcgacctgctgctcgctgactttaatggt-----
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|148952817|gb|EC898809.2|EC898809
EST:     CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAG                         CGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
genomic: CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAGgtaaacagaa ... gttattatagCGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
EST: gi|148970824|gb|EE021591.2|EE021591
EST:     CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAG                         CGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
genomic: CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAGgtaaacagaa ... gttattatagCGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
EST: gi|15427195|gb|BI543017.1|BI543017
EST:     CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAG                         CGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
genomic: CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAGgtaaacagaa ... gttattatagCGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
EST: gi|21621474|gb|BQ619480.1|BQ619480
EST:     CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAG                         CGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
genomic: CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAGgtaaacagaa ... gttattatagCGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
EST: gi|211183157|gb|FL428740.1|FL428740
EST:     CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAG                         CGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
genomic: CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAGgtaaacagaa ... gttattatagCGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
EST: gi|71435430|gb|DR816480.1|DR816480
EST:     CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAG                         CGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
genomic: CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAGgtaaacagaa ... gttattatagCGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
EST: gi|76290045|gb|DV029613.1|DV029613
EST:     CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAG                         CGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
genomic: CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAGgtaaacagaa ... gttattatagCGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
EST: gi|91052216|gb|EB162634.1|EB162634
EST:     CGAGAAGTCCGAAGTGTACAGCACTAATATGACGCAGGCTATGGGAGCAG                         CGTTGACATATAGACATGACCTCGGGATGAACTACAATTT
genomic: CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAGgtaaacagaa ... gttattatagCGTTGACATATAGACATGAACTCGGGATGAACTACAATTT
EST: gi|211478786|gb|FL377818.1|FL377818
EST:     CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAG                         CGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
genomic: CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAGgtaaacagaa ... gttattatagCGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
EST: gi|76914764|gb|DV165677.1|DV165677
EST:     CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAG                         CGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
genomic: CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAGgtaaacagaa ... gttattatagCGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
EST: gi|74234762|gb|DT642676.1|DT642676
EST:     CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAG                         CGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
genomic: CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAGgtaaacagaa ... gttattatagCGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
EST: gi|149081546|gb|EE170685.2|EE170685
EST:     CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAG                         CGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
genomic: CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAGgtaaacagaa ... gttattatagCGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
EST: gi|148967268|gb|EE018472.2|EE018472
EST:     CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAG                         CGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
genomic: CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAGgtaaacagaa ... gttattatagCGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
EST: gi|211346141|gb|FL398010.1|FL398010
EST:     CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAG                         CGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
genomic: CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAGgtaaacagaa ... gttattatagCGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
EST: gi|211266638|gb|FL405762.1|FL405762
EST:     CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAG                         CGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
genomic: CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAGgtaaacagaa ... gttattatagCGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
EST: gi|148934585|gb|EC878634.2|EC878634
EST:     CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAG                         CGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
genomic: CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAGgtaaacagaa ... gttattatagCGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
EST: gi|91876121|gb|EB406078.1|EB406078
EST:     CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAG                         CGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG
genomic: CGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAGgtaaacagaa ... gttattatagCGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGGGGCGTCCACTTCCGGTGCCGAGAGCAGCGCCGTGGAGATGGGCACCGAGAAGTCCGAAGTGTACAGCACTAACATGACGCAGGCTATGGGAGCAGgtaaacagaatgtttgcttctgtcctgtgtgcgctgcttgtagtgttaggccttgttagacgctgactgtcttatcgcattctgggcaaattggttgctg

- - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG